April 4, 2004 - April 10, 2004 Archives

Just in case you aren't as tired with the whole NCSE-violating-the-Establishment-Clause thing as I am. . .

Where purpose and function meet

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Benjamin Wiker, who was recently heard accusing Darwinists of being in panic over 'specified complexity', seems to continue his wishful thinking in this article in Crisis Magazine. There seems to be indeed a crisis but contrary to Wiker's suggestions, the crisis seems to be in the ID camp where ID's failure to deliver scientifically relevant contributions seems to have cause much confusion.
Guillermo Gonzalez, assistant professor in astronomy and fellow at the Center for (the Renewal of) Science and Culture of the Discovery Institute and Jay Richards, formerly a fellow in philosophy and theology and vice president and senior fellow at the Center for (the Renewal of) Science and Culture of the Discovery Institute recently published a book called "Privileged Planet" in which they argue for purpose in the Universe. Their arguments are very similar to those found in "Rare Earth" by Ward and Brownlee and for good reasons, Gonzalez used to work at the same University of Washington where Ward and Brownlee work and was closely involved in the development of their thesis an aspect I intend to further address in a future posting. The main difference between the two books is that in "Privileged Planet" the authors argue for 'purpose' based on the "Rare Earth" argument of probability and additionally a novel argument based on a correlation between habitability and measurability. The combination of low probability and specification (correlation) implies, using Dembski's "Design Inference", design. Gonzalez et al's presentation at the "Who is the Designer: Reasons to Believe 2003" conference was critically reviewed during the Conference at the American Scientific Affiliation 2003 Annual Meeting "The Heavens Declare the Glory of God". Kyler Kuehn presented a critical analysis of the Privileged Planet hypothesis (PPT). In a series of "Privileged Planet" postings I intent to present, explore and critique their arguments. In part 1 I describe a lecture by Gonzalez et al on April 8th 2004 in the Pacific Science Center in Seattle. A day earlier Gonzalez et al had presented their arguments at the University of Washington. Both events were co-sponsored by the Discovery Institute. I regret that I was not present during their presentation at the UW since it would be interesting to hear the opinions from astronomers and especially Ward and Brownlee. Andrea Bottaro wrote some earlier comments on the Privileged Planet on this blog.

Are “intelligent agents” supernatural?

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We have recently had the jaw dropping experience of Joe Carter stating that Forensic Science does not use "methodological naturalism" because the mind is a "supernatural" entity. However, this kind of reasoning is used by other ID advocates. Francis Beckwith has written:

ID theorists maintain that contemporary science's repudiation of intelligent agency as a legitimate category of explanation is not the result of carefully assessing ID's arguments and finding them wanting, but rather, it is the result of an a priori philosophical commitment to methodological naturalism (MN), (n4) an epistemological point of view that entails ontological materialism (OM),(n5) but which ID proponents contend is not a necessary condition for the practice of science.(n6) (p. 457, "Science and Religion Twenty Years after McLean v. Arkansas: Evolution, Public Education, and the New Challenge of Intelligent Design." Harvard Journal of Law & Public Policy 26.2 (Spring 2003: 455-499)

To paraphrase Mr. Babbage, I cannot apprehend the confusion of mind that would result in the above statement. What do ID "theorists" think that forensic science, anthropology and archeology do if not address intelligent agency as a legitimate category of explanation? Last time I looked, forensic science, anthropology and archeology were all standard science fields using "methodological naturalism". We've looked for intelligent agency in the origin of the HIV virus (and come up negative). Maybe ID "theorists" object to the fact that they deal with design by human intelligence, but science also deals with design by non-human intelligent agents, as I noted in my comment on the ability to determine that certain stone piles in rainforests were chimpanzee hammer stones, and the investigation of creative tool-making by Pacific Island ravens (Bird Brain will never mean the same thing again). Again they might object that the intelligent agents were all contemporary, and we could observe them, but we can also discern design by long vanished non-human intelligent agents, australopithecines (and Homo erectus, but they are human, although not modern).

As Francis Beckwith visits this blog, and had to discuss this issue with ID "theorists" to write the above paragraph, perhaps he could be so kind as to inform us what ID "theorists" mean by "intelligent agency" that it excludes humans, australopithecines, chimpanzees and Pacific Island Ravens.

Miss me, anyone?

I'm in the hospital with my worst-ever flare-up of Crohn's disease. I promise to spare you the disgusting details, but it has been bad enough to keep me away from an Internet connection for almost a week. That should tell you something.

But I did learn about some preliminary research that indicates that perhaps my condition results from changing the environmental conditions away from the usual coevolutionary relationship between humans and intestinal parasites. A small clinical trial tested the effect of giving Crohn's and ulcerative colitis patients porcine whipworm, Trichuris suis, and got some intriguing results. The researchers note that the initial study is too small to separate possible placebo effects, but positive responses in several patients indicate the need for a larger controlled study.

The basic gist behind this is that the porcine whipworm parasites are invasive enough to obtain an appropriate response from the gut, while being out-of-place enough in the human system that they don't pose a significant health risk of their own. The researchers also note an observed inverse relationship between incidence of Crohn's and colitis cases and prevalence of intestinal parasitic infections. If this works out, continuing maintenance of Crohn's and ulcerative colitis in at least some patients may include a routine of ingesting porcine whipworm eggs periodically. While I usually shudder at the idea of deliberate nematode ingestion, my recent experiences certainly put me in favor of giving it a try.

Squid Hox genes

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It's April, it's Minnesota, and it's snowing here. On days like this, my thoughts turn to spicy, garlicky delicacies and warm, sunny days on a lovely tropical reef—it's a squiddy day, in otherwords, and I've got a double-dose of squidblogging on this Friday afternoon, with one article on the vampire squid, Vampyroteuthis infernalis, and this one, on squid evolution and cephalopod Hox genes.

Continue reading "Squid Hox genes" (on Pharyngula)

I came across this passage in another blog, Alcaide's Cafe, written by Russell Husted. As a general rule, Russell's page is considerably more sophisticated and better written than most of its kind, but this passage came as a surprise to me. In this post, he discusses the fact that finding water and methane on Mars is not necessarily evidence of life on Mars, and on that point he is of course correct. Those things might provide evidence that microbial life was once present, or is now present, on Mars, but that is still an entirely open question. But he doesn't stop there. He seems to think that if we do find life on Mars, this will be a problem for evolution because that life, presumably, stayed at the microbial level and did not "advance" to more complex, multicellular life. He writes:

When reading Andrea Bottaro's fine post of April 6 (titled Getting Away With "heresy") where he tells telltale stories about non-orthodox ideas taking hold in mainstream biology, it reminded me some stories that took place in my field. I am taking the liberty of telling here a story from my own past with a hope it will not be found inappropriate for this forum. I guess the name of Lev Landau is known to most of the readers of this blog. He was a very prominent theoretical physicist, a Nobel laureate and a founder and a long-time leader of a group of outstanding theoretical physicists in Russia. His authority among physicists in the USSR was immense and undisputed. To argue against Dau (as he usually was referred to) one could only at one's peril. Every physicist viewed it an honor to be allowed to give a presentation at Landau's famous weekly seminar. If Landau approved the presentation it would immensely enhance the prestige of the presenter. On the other hand, if Landau disliked the thesis he would make mincemeat of the offender with a few very caustic and witty remarks. After being thus disparaged, the hapless offender had nowhere to appeal. There was in the USSR a professor of physics by the name of Pines who authored an authoritative book on X-rays technique. Once he submitted to Landau a paper which he wished to present at Landau's seminar. This paper was a theoretical treatise about Poisson coefficient. Poisson coefficient is the ratio between the relative transverse and longitudinal strains of a solid body. It had been a commonly accepted view that Poisson coefficient may have only positive values up to k=1/2. Positive value of k means that when a body is stretched along some axis, it shrinks in the transverse direction. (For example, this is stated in the famous Feynman Lectures on Physics). In fact, a thermodynamic analysis (which I performed in ‘69) shows that no law of physics forbids a negative value of k, so that k may in principle have values between -1 and +1/2 . Negative k means that a body, while being stretched along some axis, would simultaneously expand along the transverse direction. Such a behavior was, though, never observed, and to the best of my knowledge, the thermodynamic analysis I mentioned was never conducted before, so the common notion had been that k is always positive and not exceeding 1/2 . I have not read Pines's article so I don't know what his arguments were, except for the general idea - he suggested some theoretical consideration showing that solid bodies with a negative Poisson coefficient may exist. I could not read Pines's article for a simple reason - Landau derided Pines, and his article was never published and was nowhere to be found. Some of my colleagues who happened to witness the story, told that, having looked over Pines's article, Landau said, "You know, Pines, if you swap i and e in your name you get the only body in the world that expands sideways when stretching. " End of Pines's prestige and of his theory. Now jump to 1969. I had at that time a doctoral student Vitaly Balagurov. He was one of only four of my doctoral students (out of the total of 26) who failed to get the doctoral degree. (In 1970 Balagurov had to abandon his research because of family circumstances). In '69 he was conducting experiments with films of magnetic alloys deposited in strong magnetic fields. He was frustrated by the stubborn instability of the data he got while measuring stress in these films - which was the task I gave him. For a while I was very busy with some other research and kept postponing a review of his data. Finally I turned to his raw data and, to my amazement, realized that the alleged instability was caused by what seemed to be a bizarre effect - when the films were stretched along one of the axes, they seemed to expand in the transverse direction. It was hard to believe, so I set out to check the data and to find the glitch in measurements which surely must have been somewhere. Together with Balagurov, we conducted hundreds of measurements, modifying the set-ups, the conditions etc, and, after a long-long series of experiments (as far as I recall, it took a whole year) I came to the conclusion that it was a real effect - these films had a negative Poisson ratio! Of course everybody knew it was impossible - the great Landau himself said so a few years earlier and destroyed the poor Pines who dared to suggest otherwise. What could I do - to openly go against Landau and common knowledge? That was exactly what I did. I wrote an article (with Balagurov as a co-author) where not only described the experimental results but also dared to offer a model suggesting a mechanism for the observed bizarre phenomenon, and sent it to the prestigious journal of the Academy of Sciences - Fizika Tverdogo Tela (Physics of Solids). The submissions to this journal always are reviewed by at least two anonymous referees. It usually takes some time. What happened, neither Landau's prestige nor the "common knowledge" played a role - our article was published, and unusually soon - in less than two months. The "orthodox" scientific "establishment" was obviously more interested in the unusual results than in preserving prestige, orthodox views, or using the alleged mechanism of peer-review to kill unwanted data - all those malaises of science attributed to it by the ID crowd. In physics and biology alike - what counts is evidence, and that is what the ID champions have in a very short supply.

Response to John Calvert

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This past Tuesday (April 6, 2004) I gave a short 25 minute speech at a luncheon sponsored by the student activities program at the University of Missouri at Kansas City (UMKC). The other speaker at the event was John Calvert, founder of the Intelligent Design network (IDnet). Calvert is a primary spokesperson for the central ID argument that science, by seeking natural explanations, essentially embraces materialism and atheism; therefore censors the evidence for design and unfairly excludes design inferences; and thus unconstitutionally indoctrinates our children in materialism when they are taught "evolution only" in our public schools. Calvert has taken this argument to boards of education, legislators and the public all over the country since 2000. I directly addressed this primary argument, first putting it in the context of the Wedge strategy and then explaining how it misrepresents the nature of science and dismisses and insults the religious beliefs of millions of people. An outline of my talk, my presentation slides, and mp3 files of my speech itself are available at the Kansas Citizens for Science website here After my speech (I went first), Calvert prefaced his prepared remarks with the following statement: I would characterize Jack's argument against design as essentially an ad hominem attack. I don't see Jack really discussing the substance of the science relating to design. That's really where the rubber meets the road. I think you need to get there if you really want to understand intelligent design. Now in my speech I had quickly dismissed the subject of the "science" of ID in order to focus on what I considered the more important topic. While I would be glad to discuss Calvert remarks about science, I take strong exception to Calvert's remark that my argument was "essentially an ad hominem attack." It is that mischaracterization that I would like to discuss in this post.

In the first installment of EvoMath, I derived the Hardy-Weinberg Principle and discussed its significance to biology. In the second installment I will demonstrate how to test if a population deviates from Hardy-Weinberg equilibrium.

One of the more difficult conceptual problems the layperson has with biology lies in the simple word "primitive". It has many antonyms - "modern", "evolved" and "derived", and like many biological uses of ordinary words, everybody thinks they understand it, and doesn't.

I've dealt already with the argument that the NCSE website's funding by the National Science Foundation violates the Establishment Clause, and Francis Beckwith's article really makes no new points. But I have a few more thoughts about it--and about the sloppy thinking it reveals (which is pretty common among creationists).

The ID crowd just continues to push this ridiculous argument that the Understanding Evolution website, by pointing out that evolution is not necessarily in conflict with religion and that many Christians and other types of theists accept evolution without giving up their faith, violates the establishment clause. The latest is from our old friend Francis Beckwith. This argument has been completely shredded by Timothy Sandefur, in a piece that Beckwith has no doubt seen. Yet he continues to push this, on his blog and in print. I'm sure he made a few bucks with the article in the American Spectator, but I still think it's kind of silly to keep pushing an argument this silly.

In fact, I think it's time for a challenge. Frank, I know you read this blog. If you really think you have an argument here, take it to court. If you really think this is a violation of the establishment clause, file a suit. John West is making the same argument and the DI has lots and lots of money to cover the legal fees. You and David Dewolf can design the legal strategy. I predict that you won't do it, because you know that this argument would be greeted with exactly the kind of response it is due, primarily laughter. I think you know how bad this argument is, but continue to push it, and ignore the criticisms that have been made of it, because it suits the DI's public relations agenda.

Joe Carter at Evangelical Outpost has jumped into the Leiter/VanDyke fray, in a post filled with misconceptions and illogical statements. He begins:

For a legal scholar and professor of philosophy, Brian Leiter has a remarkably poor grasp of basic logic. For the past week Leiter has been bashing a defender of Intelligent Design theory using his typical rhetorical style of bullying and bluster. Instead of thinking up creative new ad hominem attacks, though, he should be paying closer attention to his reasoning.

William Dembski's latest book, The Design Revolution: Answering the Toughest Questions About Intelligent Design consists of 44 questions about intelligent design with short answers by Dembski -- each answer takes about 6 or 7 pages, on average. Critics of Dembski -- such as Mark Perakh -- who were looking forward to having their objections addressed will be disappointed. The Design Revolution is even more intellectually dishonest than I thought possible. The easy questions Dembski actually addresses are answered disingenuously; the really hard questions he avoids entirely. This book should have been titled Desperately Evading the Toughest Questions About Intelligent Design.

Disclaimer news

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A judge in Atlanta, Georgia, has refused to dismiss a lawsuit brought by a group of parents against the Cobb County School District. The parents are arguing that the district's placement of stickers bearing a "disclaimer" about evolution is illegal.

The disclaimer says "This textbook contains material on evolution. Evolution is a theory, not a fact, regarding the origin of living things. This material should be approached with an open mind, studied carefully and critically considered." The parents, who are represented by the Georgia ACLU argue that the School Board's use of this sticker violates the Establishment Clause of the First Amendment. Although I think such disclaimers are incredibly stupid, I don't think that they violate the Constitution.

Getting away with “heresy”

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Conspiracy mongering and accusations of censorship have become standard fare in the writings of even the supposedly more serious Intelligent Design advocates, perhaps paralleling their progressive realization of utter scientific irrelevance. By their own meter, in the Wedge document ID leaders confidently set themselves a goal of 100 published scientific, technical or academic articles by 2003. Since this goal has not even remotely been achieved, nor seems likely to be achievable in any distantly foreseeable future, unsubstantiated claims like:

"To question Darwinism is dangerous for all professional scholars but especially biologists." W.A. Dembski, The Myths of Darwinism, in Uncommon Dissent


"There's good reason to be afraid. Even if you're not fired from your job, you will easily be passed over for promotions." M. Behe, quoted in Harvard Political Review, 5/12/02

and hyperbolic accusations of "stifling orthodoxy" or "Stalinist repression" have understandably replaced the bold forecasts of yore.

Contrary to these accusations, however, it can be easily shown how in the last few decades evolutionary biology has seen a number of unorthodox ideas gain acceptance, probably even more than most other branches of science. The symbiotic origin of mitochondria and plastids, the catastrophic theory of the dinosaurs' extinction, the neutral theory of molecular evolution, the existence of an entire new kingdom of organisms (Archaebacteria) and punctuated equilibria are all examples of unconventional hypotheses which have become mainstream within a few years from their original formulation, based on the strength of evidence. This is not to claim that science does not suffer from a reluctance to change - just like any other human activity - but rather that, when a new idea has merit, it arguably has more chances of receiving a fair hearing in science than, say, in politics or business (let alone activities that thrive on strict adherence to tradition, like kabuki theatre or religion).

But what about ideas that actually challenge the most fundamental tenets of evolutionary theory, especially its darwinian components? Are those being censored?

Dumping on Dembski

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Having temporarily put aside the MSUP ID anthology, I've recently started making a more concerted effort to get through Dembski's The Design Revolution. I previously posted some thoughts on two especially outrageous quotes I found (upon opening the book to a random page) over at EvolutionBlog, in my entry for March 16.

So I came into my office this morning all set to unload a real sockdolager of a post on the sheer, unmitigated awfulness of Dembski's latest, only to discover that Jeffrey Shallit had beaten me to it. Sigh. As it happens though, there is so much to criticize in Dembski's book that Shallit has only scratched the surface.

I have lately been engaged in a conversation that is just making me more and more annoyed. It began with a blogger named Rusty Lopez saying,

Yet, one wonders what thoughts the likes of Eugenie Scott, Daniel Dennett, Richard Dawkins, et. al., are having as they smirk behind Miller's back.
And quoting Bill Dembski saying,
Not to put too fine a point on it, the Darwinian establishment views theistic evolution as a weak-kneed sycophant that desperately wants the respectability that comes with being a full-blooded Darwinist but refuses to follow the logic of Darwinism through to the end. It takes courage to give up the comforting belief that life on earth has a purpose. It takes courage to live without the consolation of afterlife. Theistic evolutionists lack the stomach to face the ultimate meaninglessness of life, and it is this failure of courage that makes them contemptible in the eyes of full-blooded Darwinists.

Brian Leiter has replied to VanDyke's latest response, posted on Ex Parte and as a comment here, and it is a devestating reply, to be sure. I was hoping Brian would get around to doing this, mostly because I've been too busy to do it myself. The misuse, probably born of misunderstanding and trusting Beckwith's portrayal, of Laudan, Kuhn and other philosophers of science and their positions on methodological naturalism, fairly screamed out from VanDyke's reply and Leiter corrects the misconceptions very well.

VanDyke gets himself into particular trouble, I think, with this smug citation of Laudan:

"If [Leiter] had even perused Dr. Beckwith's book he would have come in modest contact with some of the leading lights in this literature including Larry Laudan, a philosopher of science who is currently on the faculty at the University of Texas and whose greatness Leiter himself extols..."
This is a brave leap in the dark, ending with a resounding thud as he lands. Leiter is infinitely better equipped to discuss Laudan's contributions to philosophy of science and the demarcation problem than VanDyke, not only because he's actually read Laudan's work on the subject (VanDyke clearly has not) but because Laudan's office is right down the hall from Leiter's office at UT. As Leiter notes:
My colleague Larry Laudan is, needless to say, well beyond being amazed anymore by the gross misrepresentations of his views--and of issues in the philosophy of science--in law reviews and by proponents of ID. (Didn't it occur to VanDyke that I might walk down the hall and point out his nonsense to Laudan? He just rolled his eyes and chuckled).
While I still tend to think that Leiter's rhetoric is a bit overly harsh, I think he's absolutely right when he says that this is all an example of a guy (VanDyke) who simply got in way over his head, pontificating on a subject he knew virtually nothing about, and his reputation took a justifiable beating as a result. It's time for him to just take his lumps and decide that should he venture into such territory again, he'll be better prepared to defend his views than he was in this case. Unfortunately, I think, based upon his reaction so far, that rather than doing that, he's going to continue to filter this through his perceptions of persecution by the "Darwinian establishment" and continue to strike the martyr pose. And as Leiter correctly notes, this is hardly an auspicious beginning for a prospective scholar.

Mooney vs. Marburger

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There was a question in one of the comments about any responses to Marburger's reply to the Union of Concerned Scientist's report on the corruption of science policy under Bush. The answer is yes; I've said a few words about it, but the best reply is to be found on Chris Mooney's site. His summary:

In my view, there are serious problems both with Marburger's strategy for rebutting the barrage of scientific charges against the administration, and with his specific rebuttal itself. Granted, Marburger scores a couple of points against the administration's critics. But these are really glancing blows. For the most part, the UCS document still stands relatively intact.

Really, though, this is one where you need to read the details.

About a year ago, the National Center for Science Education (NCSE) circulated a statement in support of evolution to a select group of scientists. How select? They only asked scientists named Steve (or Stephanie, or some other variation) to sign it. The purpose? To mock the use of lists, recently put forward by the Discovery Institute (DI), that suggest that significant numbers of scientists questioned evolution. By limiting the eligible signatories to such a small group, it also conveyed to the public just how much more support there was for within the scientific community evolution than against. To celebrate the 1 year anniversary of Project Steve (okay, we missed it by about a month and a half), The Panda's Thumb is revisiting the project. While the NCSE did all the actual work for Project Steve, and rightfully deserves the credit for it, the original idea was spawned from the members of the TalkDesign.org website (who are closely affiliated with this blog). You can read all about Project Steve at the NCSE website. There you can find links to the actual list, the original press release, newspaper articles, and the Steve-o-meter, which is currently at 431. To read all about the project from its creators, Glenn Branch and Skip Evans, check out this Geotimes article. You can also read Eugenie Scott's take here. The following article relives the joy that was Project Steve, and discusses the appeal to authority.

The Hardy-Weinberg Principle states that a population satisfying certain primary conditions will not evolve. This result is very important because any departure from these conditions will result in an evolving population. Three scientists in the early 20th century (G.H Hardy, Wilhelm Weinberg, and W.E. Castle) independently discovered this principle which is now used as the null model of population biology.

Consider a group of interbreeding organisms (a population)…

brauer_fig3.jpgbrauer_fig6Last week I introduced Dawkins' term "designoid" with a striking example. These objects have been found in a variety of places, but the most controversial of them come from the site of putative neolithic habitations in the present Gulf of Cambay, India. The "artifacts" have been used to bolster the controversial theory that a highly developed civilization existed at the site nearly 10,000 years ago.

I just noticed (via Chad Orzel) that the Washington Monthly has another relevant post up—Kevin Drum chastises the NRO's John West for his silly article about the NCSE pushing religion, the same subject discussed here.

Drum is asking good, pointed questions, and the ensuing comments are also interesting.

Addendum: see also this followup by Drum.

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